bug fix

Author: mshahneh

modifinder/classes/Compound.py

@@ -130,11 +130,11 @@ def structure(self, value):
         if self._structure is not None:
             self._exact_mass = rdMolDescriptors.CalcExactMolWt(self._structure)
             self._distances = Chem.rdmolops.GetDistanceMatrix(self._structure)
-        if self.is_known is None:
-            self.is_known = self._structure is not None
+        if self.is_known is None and self._structure is not None:
+            self.is_known = True
 
         if self.is_known and self._structure is None:
-            self.is_known = False
+            self.is_known = None
 
     @property
     def spectrum(self):
@@ -232,8 +232,8 @@ def update(self, _structure = None, structure = None, id: str = None, _spectrum:
 
     def _parse_data(self):
         """ Parse missing and verify the data of the class"""
-        if self.is_known is None:
-            self.is_known = (self.structure is not None)
+        # if self.is_known is None:
+        #     self.is_known = (self.structure is not None)
 
         # if no id is provided, generate one
         if self.id is None:

modifinder/classes/Spectrum.py

@@ -64,7 +64,7 @@ def __init__(self, incoming_data=None, normalize_peaks = True, **kwargs):
         self.ms_mass_analyzer = None
         self.ms_dissociation_method = None
         self.spectrum_id = None
-        self.peak_fragments_map = []
+        self.peak_fragments_map = {}
 
         if incoming_data is None and len(kwargs) == 0:
             return
@@ -174,7 +174,7 @@ def clear(self):
         self.ms_mass_analyzer = None
         self.ms_dissociation_method = None
         self.spectrum_id = None
-        self.peak_fragments_map = []
+        self.peak_fragments_map = {}
 
 
     def copy(self):

modifinder/engines/annotation/MAGMaAnnotationEngine.py

@@ -41,7 +41,7 @@ def annotate(self, network: nx.DiGraph, annotate_all: bool = False, **kwargs):
         for node in network.nodes:
             compound = network.nodes[node]["compound"]
             if compound is not None and compound.is_known:
-                if annotate_all or compound.spectrum.peak_fragments_map is None:
+                if annotate_all or (compound.spectrum.peak_fragments_map is None or len(compound.spectrum.peak_fragments_map) == 0):
                     self.annotate_single(compound, modify_compound=True, **kwargs)
 
         # refine by helpers